words_probabilities {drimmR} | R Documentation |
Probability of appearance of several words at several positions of a DMM
Description
Probability of appearance of several words at several positions of a DMM
Usage
words_probabilities(words, pos, x, output_file = NULL, plot = FALSE)
Arguments
words |
A vector of characters containing words |
pos |
A vector of integer positions |
x |
An object of class |
output_file |
(Optional) A file containing the matrix of probabilities (e.g,"C:/.../PROB.txt") |
plot |
|
Value
A dataframe of word probabilities along the positions of the sequence
Author(s)
Victor Mataigne, Alexandre Seiller
References
Barbu VS, Vergne N (2018). “Reliability and survival analysis for drifting Markov models: modelling and estimation.” Methodology and Computing in Applied Probability, 1–33. doi: 10.1007/s11009-018-9682-8, https://doi.org/10.1007/s11009-018-9682-8. Vergne N (2008). “Drifting Markov models with polynomial drift and applications to DNA sequences.” Statistical Applications in Genetics Molecular Biology , 7(1) . doi: 10.2202/1544-6115.1326, https://doi.org/10.2202/1544-6115.1326.
See Also
fitdmm, getTransitionMatrix, word_probability, word_probabilities
Examples
data(lambda, package = "drimmR")
dmm <- fitdmm(lambda, 1, 1, c('a','c','g','t'), init.estim = "freq",
fit.method="sum")
words <- c("atcgattc", "taggct", "ggatcgg")
pos <- c(100,300)
words_probabilities(words=words,pos=pos,dmm,plot=TRUE)